Clarify limitation of -with-docker in the docs [ci skip] (#3408)

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

docs/container.rst

@@ -172,9 +172,10 @@ your pipeline execution.
 Multiple containers
 -------------------
 
-It is possible to specify a different Docker image for each process definition in your pipeline script. Let's
-suppose you have two processes named ``foo`` and ``bar``. You can specify two different Docker images for them
-in the Nextflow script as shown below::
+It is possible to specify a different Docker image for each process definition in your pipeline script. However, this
+can't be done with ``-with-docker`` command line option, since it doesn't support process selectors in the ``nextflow.config`` file, and doesn't
+check for the ``container`` process directive in the pipeline script file. Let's suppose you have two processes named ``foo``
+and ``bar``. You can specify two different Docker images for them in the Nextflow script as shown below::
 
     process foo {
       container 'image_name_1'
@@ -210,6 +211,10 @@ Alternatively, the same containers definitions can be provided by using the ``ne
 
 Read the :ref:`Process scope <config-process>` section to learn more about processes configuration.
 
+After running your pipeline, you can easily check what container image each process used with the following command::
+
+    nextflow log last -f name,container
+
 Advanced settings
 -----------------